Provincial officials say the water heading into the province from Saskatchewan has crested near Portage la Prairie west of Winnipeg.
They say the water should start to recede slowly over the coming days.
Water levels will remain high on Lake Manitoba which is expected to peak in early August.
Flood water coming from the west recently prompted Manitoba to declare a state of emergency and call in the military to help people protect their homes.
The province says more than 1,000 people from the military and government departments were involved in flood preparations.